After some time I got tired drawing Y chromosome SNP trees with graphics
programs and I also wanted to get something where I can search for
haplogroup names and SNP names in a plain HTML document with the search
function in my browser.

That's why two weeks ago I started to code a database driven tree
software that can display and edit the Y chromosome tree and that logs
all the changes to the phylogeny in a database. To be honest I found
already a basic backbone structure software at http://treeeditor.com.
However there where many parts missing so I modified the code to our needs.

You can have a look at http://ytree.ftdna.com to see it working in the
"alpha version". I don't give any warranty that all data are correct
yet. However you are welcome to check it out and get the picture about
the philosophy behind this project.

When you first come to the web page it will display the full YCC tree as
it is printed on the posters that we distributed at the last FTDNA
conference at the beginning of this year. The nodes of the tree are
entirely based on the marker names and the haplogroup names are only
pulled out from a database table since they are expected to change over
time. Wherever there is a difference between the YCC and ISOGG
nomenclature the ISOGG haplogroup name is displayed next to it. You'll
still see a few quirks with this but I'm working to get them cleared out.

Whenever you click on a node with the "root" symbol, this will open a
new sub-tree which focuses on the branches below this new root. The URL
for this sub-tree can be bookmarked so that you can quickly focus on the
part of the tree that you are interested in. The marker names are linked
to the ymap Y chromosome map. I'm thinking about a way to get a link
back from ymap to ytree as well but I can't imagine how it should work
in detail right now. I'm open for suggestions.

On the top of the page you can always switch back and forth between the
YCC tree and my most current Draft tree which includes the most recent
SNPs discovered from the WTY project or from elsewhere. The nodes that
have changed are marked with a little yellow star which will gray out
the older the last change gets. So the newest changes will always appear
in bright yellow. If you hover your mouse above a star you can see the
days that have passed since the last change was done. Clicking on the
star will brig you to a table that lists all the changes that have been
recorded for this node.

I'd be happy to hear your comments and suggestions. Of course if you see
an error please report it to me so that I can fix it. Hopefully this
Ytree will be a helpful tool and not make more confusion about
nomenclature and unresolved branches. In any case I felt that I need
this tool by myself to keep track of the rapidly changing phylogenies
with the new markers that are discovered recently.

I hope this helps,

Thomas

P.S. The source code for the Ytree application is in the public domain.
It can be downloaded in the Downloads section.

Thank you very much for all that have been attending the FTDNA conference in Houston this year. For all that have not been able to follow my talks personally I have uploaded the PDF documents the downloads section.

During my recent review of new and existing SNP markers in the haplogroups E, G, I and Q I've continuously drawn working drafts which help me to understand and discover discrepancies that still need to get resolved. Over and over again I need to mention that the tree structure wasn't resolved or invented by myself. At best I try to improve and extend the major work of others and I try to collect all available information from the genetic genealogy community in a central place so that we are able to communicate the findings to the academic researchers.

The following draft tree graphics are heavily based on the YCC tree from Karafet et al. 2006 [1] and on the most current ISOGG tree 2009 [2].

Note that because I'm frequently updating the trees you may need to refresh the web page to see the latest version. Most browsers cache the graphics from the first visit. Click on the images to enlarge.

Many thanks to all voluntary participants of the genealogical testing community for sharing their testing data from deCODEme and 23andMe chips and some of them providing control samples for my evaluation test runs. Special thanks also to Elise Friedman, Dr. Dirk Schweitzer, Dr. Ken Nordtvedt, Ted Kandell, Dr. Whit Athey, Victor Villarreal and Dr. David Wilson who identified the new SNPs as useful tests for DNA genealogy, pre-selected significant samples and helped me to refine the topology by cross checking all sources. This work wouldn't have been possible without the great spreadsheets from Ann Turner and Adriano Squecco who collected the SNP data from the volunteers that payed for their own DNA tests and made them available to the public.

This draft shows a portion of the Y chromosome tree in extension to Karafet et al. [1] and the ISOGG tree [2]

I have added the recently discovered SNP markers and I implemented the topology from our latest evaluation runs. Some positions on the tree are only verified by single samples. Additionally I have marked the uncertain assignments which are either work in progress or which cannot be tested by our laboratory due to missing control samples. More information on the SNP details can also be found at Ymap.

Note that because I'm frequently updating the tree you may need to refresh the web page to see the latest version. Most browsers cache the graphics from the first visit.

Working Draft of the Y Chromosome Tree Below J-M304 by Thomas Krahn is licensed under a Creative Commons Attribution-Noncommercial 3.0 Germany License.
Many thanks to all voluntary participants of the genealogical testing community for sharing their testing data from deCODEme and 23andMe chips and some of them providing control samples for my evaluation test runs. Special thanks also to Alfred Aburto and Bonnie Schrack who identified the new SNPs as useful tests for DNA genealogy, pre-selected useful samples and helped me to refine the topology by cross checking all sources. This work wouldn't have been possible without the great spreadsheets from Ann Turner and Adriano Squecco who collected the SNP data from the volunteers that payed for their own DNA tests and made them available to the public.
The credit for discovering the importance of the L27 marker (rs34126399) goes to Dr. Roy King who has published his findings in his Spittoon article [3] on Jul. 25th 2008.

[3] King R. The Origin of Farming in Europe: A View from the Y Chromosome, The Spittoon, Date: July 25th 2008, http://spittoon.23andme.com/2008/07/25/the-origin-of-farming-in-europe-a-view-from-the-y-chromosome/

The DYS710 marker is a high frequency mutating YSTR that is very useful for near range (family) genealogy studies. Many alleles carry a N.2 micro-allele which further increases the variability of this marker. I just have fixed the bug in Ymatch which prevented entering the micro-allele, so you are able now to store the allele with- or without a microallele in your DNA-Fingerprint account.

This draft shows a portion of the Y chromosome tree in extension to Karafet et al. [1] and the ISOGG tree [2]

I have added the recently discovered SNP markers and I implemented the topology from our latest evaluation runs. Some positions on the tree are only verified by single samples. Additionally I have marked the uncertain assignments which are either work in progress or which cannot be tested by our laboratory due to missing control samples. More information on the SNP details can also be found at Ymap [3].

Note that because I'm frequently updating the tree you may need to refresh the web page to see the latest version. Most browsers cache the graphics from the first visit.

Working Draft of the Y Chromosome Tree Below R-M269 by Thomas Krahn is licensed under a Creative Commons Attribution-Noncommercial 3.0 Germany License.
Many thanks to all voluntary participants of the genealogical testing community for sharing their testing data from deCODEme and 23andMe chips and some of them providing control samples for my evaluation test runs. Special thanks also to David Reynolds who sketched out the first draft at DNA-Forums and helped me to refine the topology by cross checking all sources. This work wouldn't have been possible without the great spreadsheets from Ann Turner and Adriano Squecco who collected the SNP data and made them available to the public.

After my web server provider has switched from PHP4 to PHP5 in July users had problems to log in and new users couldn't even register. It took me a while of work to find out the actual reasons. It turned out that the SESSION variable wasn't properly stored and I had to call register_shutdown_function('session_write_close');
in Postnuke's includes/pnsession.php (right after ini_set('session.auto_start', 1);)
in order to get it working. Thanks to TiMax

Now the login and register functions should work again. Sorry for the inconvenience and thanks for your patience.

During my current work on Y chromosome markers I frequently ran into the question where exactly those markers are located. The location of the markers is often the key to understand the recombination mechanisms and if multiple markers are aligned to the same reference sequence we find out that markers with different names may in fact be one and the same location on the Y chromosome.

Looking up marker positions in public databases has been time consuming and needs a lot of knowledge in molecular biology. For this reason I have collected information about all kind of Y chromosome markers and their positions along the current HUGO reference sequence. To make this all accessible to the public I have arranged the data in a HapMap style genome browser and we have setup a webserver at Family Tree DNA so that it can be accessed at a high speed internet connection.

Just type in a marker name into the Landmark or Region field and submit the Search. Examples: M201, DYS456, or a region like Yq11.221

The browser will show the position of the marker in the Overview graphic and it will zoom at the propitiate range in the Details view. If you zoom out a little bit, you will see the markers in the neighboring region. The marker of interest will be highlighted in yellow so that you don't loose its position. If you click on the marker it will display more detailed information and sometimes a link to more external resources like NCBI or GDB. The numbering of the reference DNA sequence is exactly synchronized with other ressources like the UCSC genome browser (Human March 2006 http://genome.ucsc.edu/)

The Y chromosome browser is still under development, so essential features and markers are still missing, but I thought that it is already very helpful for the advanced DNA genealogist and I didn't want you to wait much longer before you can try it. The database already contains more than 40.000 features and it will be updated frequently. I believe that some specialist genealogists out there may find errors and missing features. We intend to make the browser as complete as possible, so please send all requests to my e-mail address: thomas@familytreedna.com . Thanks for your help and have fun exploring the Y chromosome!

I just wanted to mention that Astrid is currently in Germany and this is the last good and easy opportunity to transfer your DNA from DNA-FP to FTDNA. Astrid will fly back on Saturday this week (May 5th 2007).

So if you want to transfer your DNA to the Houston lab and didn't indicate this before, please log in into your DNAFP account and choose FTDNA-Transfer from the Main Menu. On Friday when Astrid has packed her luggage we will remove the automatic transfer option from the website. The transfer will be then much more complicated for us, so please be considerate and use this last opportunity.

For those who don't want to transfer the extracted DNA will be simply stored in Germany as promised at -20 C in a regular freezer, but we can't guarantee 100% uninterrupted frozen storage in case of a failure of the freezer because we can't fix it so quickly from here in Houston. So we recommend the storage in the automatized REMP SSS storage in Houston (see www.remp.com) for everybody who wants his DNA in a safe place.

Happy new year to all DNA-Genealogists! The DNA-Fingerprint website has successfully been transferred to the provider Variomedia.de . The most important functions are working, but there are still many bugs to resolve. The userpages and the YMatch/XMatch/MtMatch databases are working, but the Excel- and Blast functionallity still needs to be configured. Please report all bugs, so that I can fix them. I'm working on it and I'm trying my best allthough I don't have a high speed internet connection in Germany anymore!